> Another alternative is to just manually bind the windmove
> commands, as the minor mode has no functionality of its own.

Yes, this is what I did in my configuration.

> Beyond just reverting the change, which I think is too radical, I am not
> sure how this can be fixed.

It feels intuitively appropriate to me that minibuffer-local-map should
override non-buffer-local minor modes. Is that an option?